runErrorModel {SpatialDecon} | R Documentation

## Apply error model to estimate technical SD from raw counts

### Description

Based on raw counts, uses past data to estimate each raw count's log-scale SD from technical noise. Specifies different error models for different platforms.

### Usage

    runErrorModel(counts, platform = "general")

### Arguments

`counts` | vector or matrix of raw counts
`platform` | String specifying which platform was used to create "rawCounts". Default to "dsp", for digital spatial profiler/ aka GeoMx. Other options include "ncounter", "rsem", "quantile", and "st" for spatial transcriptomics/visium.

### Value

a matrix of log2-scale SDs

### Examples

    library(GeomxTools)
    datadir <- system.file("extdata", "DSP_NGS_Example_Data", package = "GeomxTools")
    demoData <- readRDS(file.path(datadir, "/demoData.rds"))

    demoData <- shiftCountsOne(demoData)
    target_demoData <- aggregateCounts(demoData)

    sd_from_noise <- runErrorModel(counts = exprs(target_demoData), platform = "dsp")
    wts <- 1 / sd_from_noise

[Package SpatialDecon version 1.4.3 Index]